Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 5N9NZ

Calculation Name: 1G0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G0X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NHL6

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2077364.863009
FMO2-HF: Nuclear repulsion 2000227.544946
FMO2-HF: Total energy -77137.318063
FMO2-MP2: Total energy -77362.911717


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:HIS)


Summations of interaction energy for fragment #1(A:2:HIS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-35.575-34.7734.733-10.945-24.591-0.066
Interaction energy analysis for fragmet #1(A:2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.037
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A4PRO00.0160.0153.804-2.2390.046-0.027-1.126-1.1310.001
4A5LYS10.8730.9735.4930.0200.0200.0000.0000.0000.000
5A6PRO0-0.023-0.0066.9180.1310.1310.0000.0000.0000.000
6A7THR0-0.037-0.0248.890-0.247-0.2470.0000.0000.0000.000
7A8LEU0-0.032-0.02012.578-0.020-0.0200.0000.0000.0000.000
8A9TRP0-0.055-0.04514.0980.0060.0060.0000.0000.0000.000
9A10ALA00.0250.00518.505-0.040-0.0400.0000.0000.0000.000
10A11GLU-1-0.830-0.84821.1640.1270.1270.0000.0000.0000.000
11A12PRO00.051-0.00624.064-0.027-0.0270.0000.0000.0000.000
12A13GLY00.0750.02125.5020.0210.0210.0000.0000.0000.000
13A14SER0-0.011-0.00523.728-0.011-0.0110.0000.0000.0000.000
14A15VAL00.0240.02425.434-0.013-0.0130.0000.0000.0000.000
15A16ILE0-0.039-0.01927.2360.0040.0040.0000.0000.0000.000
16A17THR00.0080.01930.300-0.003-0.0030.0000.0000.0000.000
17A18GLN0-0.022-0.02132.867-0.005-0.0050.0000.0000.0000.000
18A19GLY00.0350.02532.8900.0050.0050.0000.0000.0000.000
19A20SER0-0.035-0.00732.114-0.005-0.0050.0000.0000.0000.000
20A21PRO0-0.0120.00428.003-0.009-0.0090.0000.0000.0000.000
21A22VAL00.000-0.00423.8620.0180.0180.0000.0000.0000.000
22A23THR0-0.042-0.01919.857-0.043-0.0430.0000.0000.0000.000
23A24LEU0-0.0010.00518.2810.0390.0390.0000.0000.0000.000
24A25ARG10.8460.91116.281-0.184-0.1840.0000.0000.0000.000
25A26CYS0-0.052-0.02110.741-0.026-0.0260.0000.0000.0000.000
26A27GLN00.0360.01910.785-0.143-0.1430.0000.0000.0000.000
27A28GLY00.0990.0276.805-0.044-0.0440.0000.0000.0000.000
28A29GLY0-0.064-0.0486.1231.0871.0870.0000.0000.0000.000
29A30GLN00.0000.0072.167-3.178-3.0922.931-1.248-1.769-0.014
30A31GLH00.0770.0062.466-0.1673.1124.630-3.551-4.3580.013
31A32THR0-0.0560.0062.593-5.356-8.0742.1882.912-2.382-0.009
32A33GLN00.004-0.0204.538-0.262-0.199-0.001-0.009-0.0530.000
33A34GLU-1-0.868-0.9141.847-27.925-29.1347.805-3.354-3.242-0.049
34A35TYR00.0120.0065.3780.7520.851-0.0010.000-0.0980.000
35A36ARG10.8970.9457.5801.3461.3460.0000.0000.0000.000
36A37LEU00.0160.02210.2890.2120.2120.0000.0000.0000.000
37A38TYR0-0.055-0.04711.901-0.090-0.0900.0000.0000.0000.000
38A39ARG10.8020.87615.9390.2510.2510.0000.0000.0000.000
39A40GLU-1-0.830-0.90518.117-0.055-0.0550.0000.0000.0000.000
40A41LYS10.9350.96219.9780.0860.0860.0000.0000.0000.000
41A42LYS11.0001.00622.6590.1630.1630.0000.0000.0000.000
42A43THR00.0620.03919.5370.0120.0120.0000.0000.0000.000
43A44ALA00.0490.02720.3000.0300.0300.0000.0000.0000.000
44A45PRO00.022-0.00420.520-0.034-0.0340.0000.0000.0000.000
45A46TRP00.0100.00619.726-0.052-0.0520.0000.0000.0000.000
46A47ILE00.0250.03215.926-0.017-0.0170.0000.0000.0000.000
47A48THR0-0.083-0.05617.168-0.050-0.0500.0000.0000.0000.000
48A49ARG10.9430.97118.2440.2920.2920.0000.0000.0000.000
49A50ILE0-0.0300.00916.7740.0340.0340.0000.0000.0000.000
50A51PRO00.0650.03717.078-0.091-0.0910.0000.0000.0000.000
51A52GLN00.0610.01110.875-0.186-0.1860.0000.0000.0000.000
52A53GLU-1-0.944-0.97113.477-0.569-0.5690.0000.0000.0000.000
53A54LEU0-0.017-0.01915.2780.0580.0580.0000.0000.0000.000
54A55VAL00.0320.03010.4790.0680.0680.0000.0000.0000.000
55A56LYS10.9590.9869.7191.4831.4830.0000.0000.0000.000
56A57LYS10.8610.9299.8820.3690.3690.0000.0000.0000.000
57A58GLY00.0070.01411.6460.1770.1770.0000.0000.0000.000
58A59GLN0-0.025-0.01312.4510.0950.0950.0000.0000.0000.000
59A60PHE00.019-0.01212.112-0.104-0.1040.0000.0000.0000.000
60A61PRO00.0090.00818.0330.0390.0390.0000.0000.0000.000
61A62ILE0-0.0160.00021.733-0.039-0.0390.0000.0000.0000.000
62A63PRO0-0.018-0.02324.6580.0230.0230.0000.0000.0000.000
63A64SER0-0.012-0.01327.6670.0150.0150.0000.0000.0000.000
64A65ILE0-0.060-0.01226.279-0.016-0.0160.0000.0000.0000.000
65A66THR00.031-0.02529.1880.0050.0050.0000.0000.0000.000
66A67TRP00.1010.03929.6300.0010.0010.0000.0000.0000.000
67A68GLU-1-0.869-0.91328.607-0.134-0.1340.0000.0000.0000.000
68A69HIS00.0010.01424.287-0.008-0.0080.0000.0000.0000.000
69A70ALA00.0540.06924.6890.0000.0000.0000.0000.0000.000
70A71GLY0-0.011-0.01723.842-0.022-0.0220.0000.0000.0000.000
71A72ARG10.8420.92820.276-0.011-0.0110.0000.0000.0000.000
72A73TYR0-0.042-0.06017.335-0.059-0.0590.0000.0000.0000.000
73A74ARG10.8890.93813.359-0.027-0.0270.0000.0000.0000.000
74A76TYR00.0410.0386.1440.0560.0560.0000.0000.0000.000
75A77TYR0-0.0160.0041.841-2.637-3.16910.700-4.631-5.5380.010
76A78GLY00.0300.0172.1230.6190.5944.866-2.834-2.0070.006
77A79SER0-0.076-0.0612.7416.6782.1100.1314.875-0.4390.000
78A80ASP-1-0.900-0.9585.188-1.421-1.369-0.001-0.001-0.0490.000
79A81THR0-0.057-0.0307.7470.2890.2890.0000.0000.0000.000
80A82ALA0-0.0020.0063.8190.4400.6360.002-0.031-0.1660.000
81A83GLY00.0410.0504.0021.1381.5010.002-0.105-0.2600.000
82A84ARG10.8580.9082.416-6.932-4.2761.455-1.616-2.495-0.023
83A85SER00.0180.0273.353-0.0300.6170.053-0.211-0.489-0.001
84A86GLU-1-0.877-0.9484.2970.3550.4860.000-0.015-0.1150.000
85A87SER0-0.028-0.0267.7000.0630.0630.0000.0000.0000.000
86A88SER00.0230.02010.1290.0420.0420.0000.0000.0000.000
87A89ASP-1-0.853-0.92011.8910.3070.3070.0000.0000.0000.000
88A90PRO0-0.050-0.03615.565-0.013-0.0130.0000.0000.0000.000
89A91LEU00.0240.02017.8190.0200.0200.0000.0000.0000.000
90A92GLU-1-0.849-0.91919.705-0.006-0.0060.0000.0000.0000.000
91A93LEU0-0.040-0.00822.6550.0100.0100.0000.0000.0000.000
92A94VAL00.0250.00024.414-0.017-0.0170.0000.0000.0000.000
93A95VAL0-0.0190.00728.1920.0010.0010.0000.0000.0000.000
94A96THR0-0.024-0.02030.761-0.001-0.0010.0000.0000.0000.000
95A97GLY00.008-0.02834.320-0.006-0.0060.0000.0000.0000.000
96A98ALA0-0.0170.01136.104-0.003-0.0030.0000.0000.0000.000
97A99TYR0-0.016-0.00335.848-0.002-0.0020.0000.0000.0000.000
98A100ILE00.0200.00341.2060.0020.0020.0000.0000.0000.000
99A101LYS10.8380.91442.7120.0100.0100.0000.0000.0000.000
100A102PRO0-0.0160.00141.8330.0000.0000.0000.0000.0000.000
101A103THR0-0.005-0.01844.9310.0000.0000.0000.0000.0000.000
102A104LEU0-0.007-0.00442.1920.0020.0020.0000.0000.0000.000
103A105SER0-0.018-0.00246.1440.0000.0000.0000.0000.0000.000
104A106ALA00.0170.00748.2090.0020.0020.0000.0000.0000.000
105A107GLN0-0.054-0.00449.518-0.004-0.0040.0000.0000.0000.000
106A108PRO0-0.011-0.02751.5350.0030.0030.0000.0000.0000.000
107A109SER00.0560.00853.050-0.003-0.0030.0000.0000.0000.000
108A110PRO00.0480.01149.6690.0020.0020.0000.0000.0000.000
109A111VAL0-0.0310.00150.1470.0030.0030.0000.0000.0000.000
110A112VAL00.0100.00548.7920.0000.0000.0000.0000.0000.000
111A113ASN00.0050.00351.7350.0000.0000.0000.0000.0000.000
112A114SER00.0690.00949.3750.0020.0020.0000.0000.0000.000
113A115GLY0-0.074-0.03247.974-0.001-0.0010.0000.0000.0000.000
114A116GLY0-0.0030.01448.9610.0010.0010.0000.0000.0000.000
115A117ASN0-0.004-0.02046.0120.0050.0050.0000.0000.0000.000
116A118VAL00.0080.00846.419-0.003-0.0030.0000.0000.0000.000
117A119THR00.0020.00846.4650.0020.0020.0000.0000.0000.000
118A120LEU0-0.005-0.00142.665-0.003-0.0030.0000.0000.0000.000
119A121GLN00.014-0.00245.7590.0000.0000.0000.0000.0000.000
120A122CYS0-0.062-0.01038.5340.0020.0020.0000.0000.0000.000
121A123ASP-1-0.823-0.91545.0410.0020.0020.0000.0000.0000.000
122A124SER00.0360.00744.842-0.002-0.0020.0000.0000.0000.000
123A125GLN0-0.016-0.00846.9730.0000.0000.0000.0000.0000.000
124A126VAL0-0.021-0.00245.297-0.002-0.0020.0000.0000.0000.000
125A127ALA0-0.025-0.01045.8960.0030.0030.0000.0000.0000.000
126A128PHE00.0040.00040.346-0.004-0.0040.0000.0000.0000.000
127A129ASP-1-0.827-0.86338.694-0.011-0.0110.0000.0000.0000.000
128A130GLY00.0250.02037.3080.0050.0050.0000.0000.0000.000
129A131PHE0-0.008-0.02138.187-0.003-0.0030.0000.0000.0000.000
130A132ILE0-0.025-0.00633.2140.0070.0070.0000.0000.0000.000
131A133LEU0-0.0080.00636.597-0.005-0.0050.0000.0000.0000.000
132A134CYS0-0.068-0.02030.714-0.006-0.0060.0000.0000.0000.000
133A135LYS10.8570.92835.008-0.085-0.0850.0000.0000.0000.000
134A136GLU-1-0.879-0.95634.4000.0400.0400.0000.0000.0000.000
135A137GLY00.0000.00632.5840.0010.0010.0000.0000.0000.000
136A138GLU-1-0.830-0.54530.4750.0890.0890.0000.0000.0000.000
137A139ASP-1-0.800-1.14734.5950.0890.0890.0000.0000.0000.000
138A140GLU-1-1.072-1.11727.9370.1690.1690.0000.0000.0000.000
139A141HIS0-0.036-0.04824.027-0.003-0.0030.0000.0000.0000.000
140A142PRO0-0.0190.00028.5870.0040.0040.0000.0000.0000.000
141A143GLN0-0.0170.00429.643-0.007-0.0070.0000.0000.0000.000
142A145LEU00.016-0.00131.4070.0060.0060.0000.0000.0000.000
143A146ASN00.0550.03732.133-0.013-0.0130.0000.0000.0000.000
144A147SER00.0170.01535.2100.0050.0050.0000.0000.0000.000
145A148GLN0-0.018-0.01636.4410.0020.0020.0000.0000.0000.000
146A149PRO00.0280.00838.585-0.004-0.0040.0000.0000.0000.000
147A150HIS00.0180.00441.377-0.005-0.0050.0000.0000.0000.000
148A151ALA0-0.050-0.01742.984-0.001-0.0010.0000.0000.0000.000
149A152ARG10.8970.94837.912-0.021-0.0210.0000.0000.0000.000
150A153GLY00.0190.02144.5540.0000.0000.0000.0000.0000.000
151A154SER00.003-0.01245.3000.0000.0000.0000.0000.0000.000
152A155SER00.0430.01545.621-0.002-0.0020.0000.0000.0000.000
153A156ARG10.8200.90146.041-0.008-0.0080.0000.0000.0000.000
154A157ALA00.0130.02442.4170.0010.0010.0000.0000.0000.000
155A158ILE0-0.035-0.01444.462-0.001-0.0010.0000.0000.0000.000
156A159PHE0-0.001-0.00138.0690.0030.0030.0000.0000.0000.000
157A160SER00.0120.01242.749-0.003-0.0030.0000.0000.0000.000
158A161VAL0-0.036-0.00840.7160.0050.0050.0000.0000.0000.000
159A162GLY00.0350.02142.036-0.004-0.0040.0000.0000.0000.000
160A163PRO0-0.015-0.01842.4160.0030.0030.0000.0000.0000.000
161A164VAL0-0.0250.01043.3520.0040.0040.0000.0000.0000.000
162A165SER00.005-0.00443.7810.0000.0000.0000.0000.0000.000
163A166PRO00.0400.01844.8830.0010.0010.0000.0000.0000.000
164A167SER0-0.035-0.00943.270-0.001-0.0010.0000.0000.0000.000
165A168ARG10.9390.98236.625-0.092-0.0920.0000.0000.0000.000
166A169ARG10.9530.97438.450-0.061-0.0610.0000.0000.0000.000
167A170TRP0-0.047-0.04540.0240.0060.0060.0000.0000.0000.000
168A171TRP0-0.030-0.02638.746-0.005-0.0050.0000.0000.0000.000
169A172TYR00.0420.00438.7010.0060.0060.0000.0000.0000.000
170A173ARG10.9280.96536.496-0.018-0.0180.0000.0000.0000.000
171A175TYR00.028-0.00235.332-0.007-0.0070.0000.0000.0000.000
172A176ALA00.0400.02738.5690.0050.0050.0000.0000.0000.000
173A177TYR0-0.069-0.06533.668-0.004-0.0040.0000.0000.0000.000
174A178ASP-1-0.758-0.86636.678-0.033-0.0330.0000.0000.0000.000
175A179SER0-0.063-0.07834.325-0.005-0.0050.0000.0000.0000.000
176A180ASN0-0.084-0.05233.237-0.003-0.0030.0000.0000.0000.000
177A181SER0-0.069-0.05731.706-0.011-0.0110.0000.0000.0000.000
178A182PRO0-0.014-0.00528.9540.0030.0030.0000.0000.0000.000
179A183TYR0-0.097-0.05525.1850.0010.0010.0000.0000.0000.000
180A184GLU-1-0.842-0.90329.427-0.084-0.0840.0000.0000.0000.000
181A185TRP0-0.017-0.02930.6330.0090.0090.0000.0000.0000.000
182A186SER00.0260.01335.071-0.005-0.0050.0000.0000.0000.000
183A187LEU00.0000.00137.6030.0020.0020.0000.0000.0000.000
184A188PRO0-0.0170.00237.9100.0030.0030.0000.0000.0000.000
185A189SER00.0190.02239.622-0.002-0.0020.0000.0000.0000.000
186A190ASP-1-0.863-0.92342.152-0.002-0.0020.0000.0000.0000.000
187A191LEU0-0.032-0.02040.6700.0020.0020.0000.0000.0000.000
188A192LEU0-0.0050.00343.151-0.001-0.0010.0000.0000.0000.000
189A193GLU-1-0.866-0.93043.6240.0400.0400.0000.0000.0000.000
190A194LEU0-0.058-0.02544.351-0.002-0.0020.0000.0000.0000.000
191A195LEU00.0040.00846.6260.0020.0020.0000.0000.0000.000
192A196VAL0-0.009-0.01246.478-0.001-0.0010.0000.0000.0000.000
193A197LEU00.0240.01249.6080.0010.0010.0000.0000.0000.000
194A198GLY0-0.010-0.00851.5740.0030.0030.0000.0000.0000.000